Evaluation of a diverse, worldwide collection of wild, cultivated, and landrace pepper (Capsicum annuum) for resistance to Phytophthora fruit rot, genetic diversity, and population structure

Phytopathology

Volumn 105, Issue 1, 2015, Pages 110-118

  Naegele, R P ^a   Tomlinson, A J ^a   Hausbeck, M K ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSICUM ANNUUM; PHYTOPHTHORA; PHYTOPHTHORA CAPSICI;

GENETIC MARKER; MICROSATELLITE DNA;

CHROMOSOME MAP; DISEASE RESISTANCE; FRUIT; GENETIC MARKER; GENETIC VARIABILITY; GENETICS; GENOTYPE; HOST PATHOGEN INTERACTION; IMMUNOLOGY; MICROBIOLOGY; PEPPER; PHENOTYPE; PHYSIOLOGY; PHYTOPHTHORA; PLANT DISEASE; POPULATION GENETICS;

CAPSICUM; CHROMOSOME MAPPING; DISEASE RESISTANCE; FRUIT; GENETIC MARKERS; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; HOST-PATHOGEN INTERACTIONS; MICROSATELLITE REPEATS; PHENOTYPE; PHYTOPHTHORA; PLANT DISEASES;

EID: 84919346719     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-02-14-0031-R     Document Type: Article

References (46)

1. Aguilar-Melendez, A., Morrell, P. L., Roose, M. L., and Kim, S.-C. 2009. Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico. Am. J. Bot. 96:1190-1202.
2. Albrecht, E., Zhang, D., Mays, A. D., Saftner, R. A., and Stommel, J. R. 2012. Genetic diversity in Capsicum baccatum is significantly influenced by its ecogeographical distribution. BMC Genet. 13:68.
3. Barksdale, T. H. 1984. Resistance to foliar blight and crown rot of pepper caused by Phytophthora capsici. Plant Dis. 68:506.
4. Benetka, V., Novotná, K., and Štochlová, P. 2012. Wild populations as a source of germplasm for black poplar (Populus nigra L.) breeding programmes. Tree Genet. Genomes 8:1073-1084.
5. Biles, C. L., Wall, M. M., Waugh, M., and Palmer, H. 1993. Relationship of Phytophthora fruit rot to fruit maturation and cuticle thickness of new Mexican-type peppers. Phytopathology 83:607-611.
6. Brachi, B., Faure, N., Horton, M., Flahauw, E., Vazquez, A., Nordborg, M., Bergelson, J., Cuguen, J., and Roux, F. 2010. Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet. 6:e1000940.
7. Candole, B. L., Conner, P. J., and Ji, P. 2010. Screening Capsicum annuum accessions for resistance to six isolates of Phytophthora capsici. HortScience 45:254-259.
8. Chen, X., Min, D., Yasir, T. A., and Hu, Y.-G. 2012. Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PLoS One 7:e44510.
9. Courtois, B., Frouin, J., Greco, R., Bruschi, G., Droc, G., Hamelin, C., Ruiz, M., Clément, G., Evrard, J.-C., van Coppenole, S., Katsantonis, D., Oliveira, M., Negrão, S., Matos, C., Cavigiolo, S., Lupotto, E., Piffanelli, P., and Ahmadi, N. 2012. Genetic diversity and population structure in a European collection of rice. Crop Sci. 52:1663.
10. Diamanti, J., Capocasa, F., Balducci, F., Battino, M., Hancock, J., and Mezzetti, B. 2012. Increasing strawberry fruit sensorial and nutritional quality using wild and cultivated germplasm. PLoS One 7:e46470.
11. Evanno, G., Regnaut, S., and Goudet, J. 2005. Detecting the number of clusters of individuals using the software structure: A simulation study. Mol. Ecol. 14:2611-2620.
12. Falush, D., Stephens, M., and Pritchard, J. K. 2003. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164:1567-1587.
13. Fonseca, R. M., Lopes, R., Barros, W. S., Lopes, M. T. G., and Ferreira, F. M. 2008. Morphologic characterization and genetic diversity of Capsicum chinense Jacq. accessions along the upper Rio Negro-Amazonas. Crop Breed. Appl. Biotechnol. 8:187-194.
14. Foster, J. M., and Hausbeck, M. K. 2010. Resistance of Pepper to Phytophthora crown, root, and fruit rot is affected by isolate virulence. Plant Dis. 94:24-30.
15. Granke, L. L., Quesada-Ocampo, L. M., Lamour, K., and Hausbeck, M. Advances in research on Phytophthora capsici on vegetable crops in the United States. Plant Dis. 96:1588-1600.
16. Greenleaf, W. 1985. Pepper breeding. Pages 68-80 in: Breeding Vegetable Crops. Springer, New York.
17. Hale, M. L., Burg, T. M., and Steeves, T. E. 2012. Sampling for microsatellitebased population genetic studies: 25 to 30 Individuals per population is enough to accurately estimate allele frequencies. PLoS One 7:e45170.
18. Hartl, D. L., and Clark, A. G. 2007. Principles of Population Genetics, 4th ed. Sinauer Associates, Inc. Publishers, Sunderland, MA.
19. Hernández-Verdugo, S., Luna-Reyes, R., and Oyama, K. 2001. Genetic structure and differentiation of wild and domesticated populations of Capsicum annuum (Solanaceae) from Mexico. Plant Syst. Evol. 226:129-142.
20. Hill, T. A., Ashrafi, H., Reyes-Chin-Wo, S., Yao, J., Stoffel, K., Truco, M.-J., Kozik, A., Michelmore, R. W., and Van Deynze, A. 2013. Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene pepper GeneChip. PLoS One 8:e56200.
21. Ibiza, V. P., Blanca, J., Cañizares, J., and Nuez, F. 2012. Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region. Genet. Resour. Crop Evol. 59:1077-1088.
22. Jones, D., Jones, G. A., Hagen, T., and Creech, E. 1985. Wild species of Nicotiana as a new source of tobacco resistance to the tobacco hornworm Manduca sexta. Entomol. Exp. Appl. 38:157-164.
23. Kang, H. M., Zaitlen, N. A., Wade, C. M., Kirby, A., Heckerman, D., Daly, M. J., and Eskin, E. 2008. Efficient control of population structure in model organism association mapping. Genetics 178:1709-1723.
24. Kimble, K., and Grogan, R. 1960. Resistance to Phytophthora root rot in pepper. Phytopathology 50:642-642.
25. Konisho, K., Minami, M., Matsushima, K., and Nemoto, K. 2005. Phylogenetic relationship and species identification by RAPD analysis in genus Capsicum. Hortic. Res. (Japan) 4:259-264.
26. Liu, K., and Muse, S. V. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129.
27. McGregor, C., Waters, V., Nambeesan, S., MacLean, D., Candole, B. L., and Conner, P. 2011. Genotypic and phenotypic variation among pepper accessions resistant to Phytophthora capsici. HortScience 46:1235-1240.
28. Minamiyama, Y., Tsuro, M., Kubo, T., and Hirai, M. 2007. QTL Analysis for resistance to Phytophthora capsici in pepper using a high density SSR-based map. Breed. Sci. 57:129-134.
29. Moses, M., and Umaharan, P. 2012. Genetic structure and phylogenetic relationships of Capsicum chinense. J. Am. Soc. Hortic. Sci. 137:250-262.
30. Naegele, R. P., Ashrafi, H., Hill, T. A., Reyes Chin-Wo, S., Van Deynze, A. E., and Hausbeck, M. K. 2014. QTL mapping of fruit rot resistance to the plant pathogen Phytophthora capsici Leonian in a recombinant inbred line Capsicum annuum L. population. Phytopathology 104:479-483.
31. Oyama, K., Hernández-Verdugo, S., Sánchez, C., González-Rodríguez, A., Sánchez-Peña, P., Garzón-Tiznado, J. A., and Casas, A. 2006. Genetic structure of wild and domesticated populations of Capsicum annuum (Solanaceae) from northwestern Mexico analyzed by RAPDs. Genet. Resour. Crop Evol. 53:553-562.
32. Pacheco-Olvera, A., Hernández-Verdugo, S., Rocha-Ramírez, V., González-Rodríguez, A., and Oyama, K. 2012. Genetic diversity and structure of pepper (Capsicum annuum L.) from Northwestern Mexico analyzed by microsatellite markers. Crop Sci. 52:231.
33. Perry, L., Dickau, R., Zarrillo, S., Holst, I., Pearsall, D. M., Piperno, D. R., Berman, M. J., Cooke, R. G., Rademaker, K., Ranere, A. J., Raymond, J. S., Sandweiss, D. H., Scaramelli, F., Tarble, K., and Zeidler, J. A. 2007. Starch fossils and the domestication and dispersal of chili peppers (Capsicum spp. L.) in the Americas. Science 315:986-988.
34. Pickersgill, B. 1997. Genetic resources and breeding of Capsicum spp. Euphytica 96:129-133.
35. Pritchard, J. K., Stephens, M., and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
36. R Development Core Team. 2012. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. http://www.r-project.org/
37. Rodriguez, J. M., Berke, T., Engle, L., and Nienhuis, J. 1999. Variation among and within Capsicum species revealed by RAPD markers. Theor. Appl. Genet. 99:147-156.
38. Sage-Palloix, A. M., Jourdan, F., Phaly, T., Nemouchi, G., Lefebvre, V., and Palloix, A. 2007. Analysis of Diversity in Pepper Genetic Resources: Distribution of Horticultural and Resistance Traits in the INRA Pepper Germplasm. Pages 33-42 in: Progress in Research on Capsicum and Eggplant. K. Niemirowicz-Szezytt, ed. Proceedings of the XIIth Eucarpia Meeting, Warsaw, Poland.
39. Saini, S. S., and Sharma, P. P. 1978. Inheritance of resistance to fruit rot (Phytophthora capsici Leon.) and induction of resistance in bell pepper (Capsicum annuum L.). Euphytica 27:721-723.
40. Spooner, D. M., and Bamberg, J. B. 1994. Potato genetic resources: Sources of resistance and systematics. Am. Potato J. 71:325-337.
41. Sy, O., Bosland, P. W., and Steiner, R. 2005. Inheritance of Phytophthora stem blight resistance as compared to Phytophthora root rot and Phytophthora foliar blight resistance in Capsicum annuum L. J. Am. Soc. Hortic. Sci. 130:75-78.
42. Wahyuni, Y., Ballester, A.-R., Tikunov, Y., Vos, R. C. H. de, Pelgrom, K. T. B., Maharijaya, A., Sudarmonowati, E., Bino, R. J., and Bovy, A. G. 2013. Metabolomics and molecular marker analysis to explore pepper (Capsicum sp.) biodiversity. Metabolomics 9:130-144.
43. Walker, S. J., and Bosland, P. W. 1999. Inheritance of Phytophthora root rot and foliar blight resistance in pepper. J. Am. Soc. Hortic. Sci. 124:14-18.
44. Waterhouse, G. M. 1963. Key to the Species of Phytophthora de Bary. Commonwealth Mycological Society, Kew, Surrey, UK.
45. Xu, J., Ranc, N., Muños, S., Rolland, S., Bouchet, J.-P., Desplat, N., Paslier, M.-C. L., Liang, Y., Brunel, D., and Causse, M. 2013. Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theor. Appl. Genet. 126:567-581.
46. Zhao, K., Tung, C.-W., Eizenga, G. C., Wright, M. H., Ali, M. L., Price, A. H., Norton, G. J., Islam, M. R., Reynolds, A., Mezey, J., McClung, A. M., Bustamante, C. D., and McCouch, S. R. 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2:467.